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Articles 31 - 44 of 44
Full-Text Articles in Genetics
Intracellular Levels Of Centrin2, Xpc, & Hhr23b Increase After Dna Damage, Nicholas A. Rowland
Intracellular Levels Of Centrin2, Xpc, & Hhr23b Increase After Dna Damage, Nicholas A. Rowland
Honors Capstones
Capstone submitted as a graduate requirement for the BSU Honors Program.
U-Statistics-Based Tests For Multiple Genes In Genetic Association Studies, Zhi Wei, Mingyao Li Phd, Timothy Rebbeck, Hongzhe Li
U-Statistics-Based Tests For Multiple Genes In Genetic Association Studies, Zhi Wei, Mingyao Li Phd, Timothy Rebbeck, Hongzhe Li
UPenn Biostatistics Working Papers
Abstract: As our understanding of biological pathways and the genes that regulate these pathways increases, consideration of these biological pathways has become an increasingly important part of genetic and molecular epidemiology. Pathway-based genetic association studies often involve genotyping of variants in genes acting in certain biological pathways. Such pathway-based genetic association studies can potentially capture the highly heterogeneous nature of many complex traits, with multiple causative loci and multiple alleles at some of the causative loci. In this paper, we develop two nonparametric test statistics that consider simultaneously the effects of multiple markers. Our approach, which is based on data-adaptive …
Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi
Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi
Dartmouth Scholarship
Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of …
Variation In Molybdenum Content Across Broadly Distributed Populations Of Arabidopsis Thaliana Is Controlled By A Mitochondrial Molybdenum Transporter (Mot1), Ivan Baxter, Balasubramaniam Muthukumar, Hyeong Cheol Park, Peter Buchner, Brett Lahner, John Danku, Keyan Zhao, Joohyun Lee, Malcolm J. Hawkesford, Mary Lou Guerinot, David E. Salt
Variation In Molybdenum Content Across Broadly Distributed Populations Of Arabidopsis Thaliana Is Controlled By A Mitochondrial Molybdenum Transporter (Mot1), Ivan Baxter, Balasubramaniam Muthukumar, Hyeong Cheol Park, Peter Buchner, Brett Lahner, John Danku, Keyan Zhao, Joohyun Lee, Malcolm J. Hawkesford, Mary Lou Guerinot, David E. Salt
Dartmouth Scholarship
Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by variation in a mitochondrially localized transporter (Molybdenum Transporter 1 - MOT1) that belongs to the sulfate transporter superfamily. A deletion in the MOT1 promoter is strongly associated with low shoot Mo, occurring in seven of the accessions with the lowest shoot content of Mo. Consistent with the low Mo phenotype, MOT1 expression in low Mo accessions …
The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs
The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs
Biology Department Faculty Works
BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …
An Improved Method For Predicting The Accuracy Of Genetic Stock Identification, Eric C. Anderson, Robin Waples, Steven T. Kalinowski
An Improved Method For Predicting The Accuracy Of Genetic Stock Identification, Eric C. Anderson, Robin Waples, Steven T. Kalinowski
United States Department of Commerce: Staff Publications
Estimating the accuracy of genetic stock identification (GSI) that can be expected given a previously collected baseline requires simulation. The conventional method involves repeatedly simulating mixtures by resampling from the baseline, simulating new baselines by resampling from the baseline, and analyzing the simulated mixtures with the simulated baselines. We show that this overestimates the predicted accuracy of GSI. The bias is profound for closely related populations and increases as more genetic data (loci and (or) alleles) are added to the analysis. We develop a new method based on leave-one-out cross validation and show that it yields essentially unbiased estimates of …
Optimizing Qpcr For The Quantification Of Periodontal Pathogens In A Complex Plaque Biofilm, Sreenatha S. Kirakodu, M. Govindaswami, Michael John Novak, Jeffrey L. Ebersole, Karen F. Novak
Optimizing Qpcr For The Quantification Of Periodontal Pathogens In A Complex Plaque Biofilm, Sreenatha S. Kirakodu, M. Govindaswami, Michael John Novak, Jeffrey L. Ebersole, Karen F. Novak
Center for Oral Health Research Faculty Publications
Quantitative PCR (qPCR) has recently been used to quantify microorganisms in complex communities, including dental plaque biofilms. However, there is variability in the qPCR protocols being used. This study was designed to evaluate the validity of two of these variables with the intent of developing a more standardized qPCR protocol. The two variables evaluated were (1) the use of DNA content versus actual cell counts to estimate bacterial numbers in mixed plaque samples and (2) the effectiveness of three different universal primers versus species specific primers in amplifying specific target pathogens in these samples. Results lead to the development of …
High Rate Of Recent Transposable Element–Induced Adaptation In Drosophila Melanogaster, Josefa Gonzalez, Kapa Lenkov, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov
High Rate Of Recent Transposable Element–Induced Adaptation In Drosophila Melanogaster, Josefa Gonzalez, Kapa Lenkov, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that …
Speciation Within Bonneted Bats (Genus Eumops): The Complexity Of Morphological, Mitochondrial, And Nuclear Data Sets In Systematics, Molly M. Mcdonough, Loren K. Ammerman, Robert M. Timm, Hugh H. Genoways, Peter A. Larsen, Robert J. Baker
Speciation Within Bonneted Bats (Genus Eumops): The Complexity Of Morphological, Mitochondrial, And Nuclear Data Sets In Systematics, Molly M. Mcdonough, Loren K. Ammerman, Robert M. Timm, Hugh H. Genoways, Peter A. Larsen, Robert J. Baker
University of Nebraska State Museum: Mammalogy Papers
We phylogenetically analyze 705 base pairs of the cytochrome-b gene and 351 amplified fragment length polymorphism (AFLP) bands from populations of the karyotypically variable Wagner’s bonneted bat, Eumops glaucinus, and the Florida bonneted bat, Eumops floridanus (Chiroptera: Molossidae). Three karyotypes have been documented across the range of E. glaucinus, and we report that the karyotype from Cuba is morphologically similar to that from Jamaica. A 4th karyotype is present in specimens from western Ecuador. Three distinct lineages are present in both the cytochrome-b and AFLP trees. One lineage is restricted to western Ecuador and exhibits cytochrome-b …
Quantitative Trait Locus Mapping For Seed Mineral Concentrations In Two Arabidopsis Thaliana Recombinant Inbred Populations, Brian M. Waters, Michael A. Grusak
Quantitative Trait Locus Mapping For Seed Mineral Concentrations In Two Arabidopsis Thaliana Recombinant Inbred Populations, Brian M. Waters, Michael A. Grusak
Department of Agronomy and Horticulture: Faculty Publications
Biofortification of foods, achieved by increasing the concentrations of minerals such as iron (Fe) and zinc (Zn), is a goal of plant scientists. Understanding genes that influence seed mineral concentration in a model plant such as Arabidopsis could help in the development of nutritionally enhanced crop cultivars. Quantitative trait locus (QTL) mapping for seed concentrations of calcium (Ca), copper (Cu), Fe, potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and Zn was performed using two recombinant inbred line (RIL) populations, Columbia (Col) × Landsberg erecta (Ler) and Cape Verde Islands (Cvi) × Ler, grown …
Whole-Plant Mineral Partitioning Throughout The Life Cycle In Arabidopsis Thaliana Ecotypes Columbia, Landsberg Erecta, Cape Verde Islands, And The Mutant Line Ysl1ysl3, Brian M. Waters, Michael A. Grusak
Whole-Plant Mineral Partitioning Throughout The Life Cycle In Arabidopsis Thaliana Ecotypes Columbia, Landsberg Erecta, Cape Verde Islands, And The Mutant Line Ysl1ysl3, Brian M. Waters, Michael A. Grusak
Department of Agronomy and Horticulture: Faculty Publications
Minimal information exists on whole-plant dynamics of mineral flow through Arabidopsis thaliana or on the source tissues responsible for mineral export to developing seeds. Understanding these phenomena in a model plant could help in the development of nutritionally enhanced crop cultivars. A whole-plant partitioning study, using sequential harvests, was conducted to characterize growth and mineral concentrations and contents of rosettes, cauline leaves, stems, immature fruit, mature fruit hulls, and seeds of three WT lines (Col-0, Ler, and Cvi) and one mutant line (Col-0::ysl1ysl3). Shoot mineral content increased throughout the life cycle for all minerals, although tissue-specific …
Ancient Dna Identification Of Early 20th Century Simian T-Cell Leukemia Virus Type 1, Sebastien Calvignac, Jean-Michel Terme, Shannon M. Hensley, Pierre Jalinot, Alex D. Greenwood, Catherine Hanni
Ancient Dna Identification Of Early 20th Century Simian T-Cell Leukemia Virus Type 1, Sebastien Calvignac, Jean-Michel Terme, Shannon M. Hensley, Pierre Jalinot, Alex D. Greenwood, Catherine Hanni
Biological Sciences Faculty Publications
The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to …
United States Regulation Of Stem Cell Research: Recasting Government's Role And Questions To Be Resolved, Owen C. B. Hughes, Alan L. Jakimo, Michael J. Malinowski
United States Regulation Of Stem Cell Research: Recasting Government's Role And Questions To Be Resolved, Owen C. B. Hughes, Alan L. Jakimo, Michael J. Malinowski
Journal Articles
This article directly addresses the stem cell controversy, but also the broader history and norms regarding the roles of federal and state government in U.S. science research funding.
Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman
Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman
School of Biological Sciences: Faculty Publications
The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic …